Molecular Playground/Hexameric ClpX

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program, and on display at the Molecular Playground with the banner "ClpX ‘spring cleans’ by dumping some proteins and refolding others."

Warning: Please close other Jmol applications or websites because some scenes are memory-intensive.

Introduction
ClpX functions as a molecular chaperone that unfolds native proteins, and as a protein degradation machinery when it forms a complex with the protease ClpP. Six ClpX monomers form a homohexamer that resembles a donut ring (electron micrographs). The top of the ring contain regions that assist in recognizing specific protein motifs. These proteins are unfolded through the central pore, and sent out of the bottom of the ring.

ClpX belongs to the AAA+ (ATPases Associated with diverse cellular Activities) family of proteins which require chemical energy from ATP hydrolysis for mechanical activity. The crystal structure of hexameric ClpX without ATP and with ATP from Escherichia coli was solved in 2009. Before that, there was only a monomeric crystal structure of ClpX from Helicobacter pylori, therefore information about the mechanistic abilities of hexameric ClpX was limited. The repetitive motion of hexameric ClpX during ATP hydrolysis can be animated using these known hexameric ClpX crystal structures (restore initial morphing movie of Hexameric ClpX ).



Hexameric Structure of ClpX
Hexameric ClpX has a highly  conserved central pore, as well as conserved interfaces between subunits/chains.

The central pore contains staggered loops along the pore channel known as pore-1 (GYVG) loops, pore-2 loops, and RKH loops (not shown). Loops at the top of the hexamer help recognize specific protein motifs. The other loops coordinate to denature and transport proteins through the pore channel. Loops at the bottom of the hexamer interact with the ClpX-partner protease, ClpP, and passes on the denatured proteins for degradation into short peptides.

Hexameric ClpX consist of staggered monomers that interface to form a near 2-fold rotational symmetry. Each monomeric subunit consist of a large AAA+ domain, small AAA+ domain, and a linker that joins the two domain.

Even though the structure is literally a homo-hexamer, the subunits are structurally heterogenous. Two distinct types of subunits have been distinguished based on the bearings of the large and small AAA+ domains, as a result of the flexibility of the linker connecting those two domains. When large AAA+ domains are lined in the same orientation, it is obvious that positions of the respective small AAA+ domains vary significantly (Type-1 subunit | Type-2 subunit ).

The positioning of Leucine 317 in the linker region is responsible for the availability of an ADP (or ATP) binding site. Leucine 317 in Type-1 subunits contacts the adenine base of the nucleotide ADP within the loop of the linker, while Leucine 317 in Type-2 subunits faces the opposite direction, causing conformation changes that prevents ADP binding. As a result,Type-1 subunits have binding sites for ADP (or ATP), and Type-2 subunits cannot bind ADP (or ATP). There are altogether four Type-1 subunits and two Type-2 subunits in a hexameric ClpX, fashioned in a cyclic 1-1-2-1-1 manner, giving a sum of only four sites for ATP/ADP nucleotide binding instead of six sites typical of AAA+ hexameric ATPases. This is not surprising because of previous experimental findings that ClpX hexamer bind a maximum number of four ATP only.

Summarily, the above described structural characteristics of hexameric ClpX help explain the mechanistic motion of hexameric ClpX that is needed to unfold proteins (restore initial morphing movie ).

My Research Interest
Currently, ClpX is best known as the partner of ClpP in the proteolytic ClpXP complex, and its roles in the control of bacterial cell cycle.

My overall research goal at the Chien Lab at the University of Massachusetts Amherst is to determine the recognition specificity of ClpX and study its influence beyond cell cycle regulation.

Main References for this Proteopedia page
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Glynn et al. Cell (2009) 139 (4): 744-56.

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. (2010) Nucleic Acids Res; DOI: 10.1093/nar/gkq399; PMID: 20478830.

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. WG Krebs, M Gerstein (2000) Nucleic Acids Res 28: 1665-75.

Acknowledgement
Thank you Professor Emeritus Eric Martz for taking all my questions and your kind help with advanced ways to solve problems with developing this page.